Alex Smith spent part of practice Tuesday barking out commands from the shotgun formation. His mission was to point out where the defensive pressure was coming from on third-and-long, communicate with center Eric Heitmann and redirect the pass protection, if necessary.

Smith and the 49ers handled things just a tad differently in such situations last season: It was called winging it.

The 49ers’ new level of sophistication is the result of — get this — a second consecutive season with the same offensive system. The whiff of continuity means they can spend their organized team activities this week doing more than flipping to Page 1 of their playbook. They’re refining what’s already in place.

Or, to put it in Raye-ese: “We’ve expedited that part of it so we don’t have to spend as much time on the rudiments of what we are doing.”

Raye cited the example of having a year’s worth of 2009 film to review. The film clips provide a teaching tool that was unavailable to the coaching staff a year ago when everything was new.

“We can identify what they are doing, good and bad, and it helps us tremendously,” Raye said.

Of course, getting the 49ers’ offense up to speed remains a mammoth undertaking. They finished 27th in the NFL last season in total yards and ranked 29th in third-down efficiency.

But much of the improvement hinges on Smith, who must do a better job of seeing the field. Raye noted how much responsibility falls on the shoulders of quarterbacks such as Peyton Manning and Tom Brady and how deftly those passers direct traffic out of the shotgun.

It’s because they understand the system.

“The quarterback has the ultimate call, because there are some things, in assessing the top of the defense, that the center can’t see,” Raye said. “At some point, it falls into the lap of the quarterback.”

It’s still a fairly basic operation at these OTAs, but this marks the first time in seven seasons that the 49ers aren’t learning a new language. Raye is the first offensive coordinator to get back-to-back seasons since Greg Knapp (2001-03).

Raye’s return engagement explains how Smith wound up leading his teammates in Tuesday’s lesson about third-down pass protection.

“A year ago, we couldn’t even have attempted that,” Raye said. “We were flying by the seat of our pants, so to speak.”

Smith said: “It’s a completely different mindset. I’m absolutely confident now. I know where the protections are. I know what’s expected of me. I know when I can take my shots, when I can gamble a little bit.”

Smith not only knows Raye’s offense but also knows Raye. The two spent extensive time in the coach’s office during the offseason to talk about what to keep and what to throw out from the ’09 playbook.

Such feedback is no small step for Smith, who tends to let the coaches call the shots. Raye and coach Mike Singletary have urged the quarterback to be more vocal in the game-planning process.

“His personality doesn’t lend itself to being that kind of person, but we’ve spent a lot of time since February just talking football one-on-one,” Raye said. “He expressed some things that he wanted to be changed, some things he thought were better, and we came to a happy medium.

“I told him, it’s democratic, but it isn’t 50-50. I’m going to make the last call on most of it.”

Patrick Willis thrilled a young cancer patient after practice. As the Pro Bowl linebacker came off the field, he stopped to chat with Brandon Dale, 15, and his family, who attended the session as guests of the 49ers. During the length of their conversation, Willis never stopped signing autographs for Brandon, and when he ran out of things to sign, Willis took off his gloves and signed those, too.

Brandon, who lives in Santa Clara, has advanced liver cancer, and his father, Andy, said that doctors are “not optimistic that he will be with us much longer.” But he said doctors have also told him that “even a smile can help boost his immune system.”

On Tuesday, his immune system was as strong as a linebacker.

Rookie receiver Jared Perry, who had travel issues a day earlier, arrived for at the OTAs and took part in practice. Still absent were linebacker Manny Lawson, cornerback Shawntae Spencer, cornerback Nate Clements, nose tackle Aubrayo Franklin, defensive lineman Kentwan Balmer, running back Michael Robinson and linebacker Keaton Kristick.

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